Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,451,190 T→C 47.2% N181N (AAT→AAC)  hdfR → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,451,1900TC47.2% ‑0.5 / 44.5 53N181N (AAT→AAC) hdfRDNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (10/18);  new base C (10/15);  total (20/33)
Fisher's exact test for biased strand distribution p-value = 7.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTGGGATATTTCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGAGGCAGGTTTGATCGGTGCTGACGA  >  minE/2451127‑2451255
                                                               |                                                                 
gCTGGGATATTTCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCt                                                              >  1:15234/1‑69 (MQ=255)
        atTTCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      <  1:976547/69‑1 (MQ=255)
        atTTCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      <  1:3411961/69‑1 (MQ=255)
        atTTCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      <  1:2156648/69‑1 (MQ=255)
         tttCTCTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      >  1:206174/1‑68 (MQ=255)
         tttCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      >  1:75692/1‑68 (MQ=255)
         tttCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      <  1:3127889/68‑1 (MQ=255)
         tttCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      <  1:457528/68‑1 (MQ=255)
         tttCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      <  1:2221305/68‑1 (MQ=255)
         tttCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      <  1:1710124/68‑1 (MQ=255)
         tttCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      <  1:922718/68‑1 (MQ=255)
         tttCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      >  1:1507101/1‑68 (MQ=255)
         tttCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      >  1:1465173/1‑68 (MQ=255)
            cACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTg                                                  >  1:55826/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGGCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTgg                                                 >  1:1685611/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTgg                                                 >  1:2853748/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTgg                                                 >  1:3053711/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTgg                                                 >  1:971105/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTgg                                                 >  1:90824/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTgg                                                 >  1:2182877/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTgg                                                 >  1:3371218/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTgg                                                 >  1:1172489/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTgg                                                 >  1:1582342/1‑69 (MQ=255)
             aCTTTAGCGCTTTATACCAGTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACTAGAGTg                                                  >  1:242975/1‑68 (MQ=255)
                     gcTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAg                                          <  1:3146717/68‑1 (MQ=255)
                     gcTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAg                                          <  1:717934/68‑1 (MQ=255)
                     gcTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAg                                          <  1:358810/68‑1 (MQ=255)
                     gcTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAg                                          <  1:2641164/68‑1 (MQ=255)
                     gcTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAg                                          <  1:747966/68‑1 (MQ=255)
                     gcTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAg                                          <  1:2436087/68‑1 (MQ=255)
                     gcTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAg                                          <  1:829004/68‑1 (MQ=255)
                     gcTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAg                                          <  1:1529888/68‑1 (MQ=255)
                       tttATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTg                                                      <  1:3391371/54‑1 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:719980/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:631109/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:73926/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:1135393/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:836912/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:402552/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:1052952/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:295620/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:1179575/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:250233/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:1200516/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:1210886/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:2145627/45‑3 (MQ=255)
                                gTGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACt                                                        <  1:435052/43‑1 (MQ=38)
                                 tGCCCCTTCTAAACTAAAGGGAGATCTTAACTATCTGCGACtag                                                      <  1:83788/44‑3 (MQ=38)
                                                     gagaTCTTAATTATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGa                          >  1:3047577/1‑52 (MQ=255)
                                                     gagaTCTTAATTATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGa                          >  1:2940144/1‑52 (MQ=255)
                                                     gagaTCTTAATTATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGa                          >  1:2870861/1‑52 (MQ=255)
                                                      agaTCTTAATTATCTGCGACTTGAGTGGGGGCCAg                                          <  1:424934/35‑1 (MQ=255)
                                                          cTTAATTATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGAGGCAGGTTTGATCGGTGCTGa     >  1:1758781/1‑68 (MQ=255)
                                                               ttATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGAGGCAGGTTTGATCGGTGCTGACGa  <  1:2269785/66‑1 (MQ=255)
                                                               ttATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGAGGCAGGTTTGATCGGTGCTGACGa  <  1:2451129/66‑1 (MQ=255)
                                                               ttATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGAGGCAGGTTTGATCGGTGCTGACGa  <  1:2724884/66‑1 (MQ=255)
                                                               ttATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGAGGCAGGTTTGATCGGTGCTGACGa  <  1:349483/66‑1 (MQ=255)
                                                               |                                                                 
GCTGGGATATTTCACTTTAGCGCTTTATACCAGTGCCCCTTCAAAACTAAAGGGAGATCTTAATTATCTGCGACTTGAGTGGGGGCCAGATTTTCAACAGCATGAGGCAGGTTTGATCGGTGCTGACGA  >  minE/2451127‑2451255

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A